Research / Single-molecule biophysics

Single-molecule biophysics and epigenetics

New imaging- and physics-based techniques offer a powerful set of tools to reveal the inner workings of molecular machines as they perform mechanical tasks. I built and used an optical trap instrument to reveal the mechanisms by which RNA polymerase II overcomes the barrier presented by nucleosomes (Hodges et al., Science, 2009; see publications). I also used similar techniques to characterize the kinetic mechanisms of other molecular machines, including the ribosome (Wen et al, Nature, 2008) and intracellular proteases (Maillard et al, Cell, 2011). I helped analyze individual transcription events based on atomic force microscopy, and integrated this work with a FRET-based assay to characterize the stability of transcribed nucleosomes (Bintu et al., NSMB, 2011). Throughout these works, I developed kinetic models to relate molecular-scale motions to biological function. These studies provide valuable insight into the fundamental biophysical mechanisms that support biological function, and remain the best experimental approaches for understanding the physics of small length and energy scales, the regime where these factors operate in the cell.

Much work is needed to transform epigenetics and chromatin biology into scientific fields based on physical principles. Revealing how these simple enzymatic activities are coupled together to achieve complex biological regulation will require experiments with intact chromatin and the full set of factors that act on it in living cells. To characterize the underlying molecular substeps of chromatin remodeling, we are performing imaging experiments to follow single BAF/PBAF complexes in living cells.

Planning for the lab is happening now. If you are interested in the research we are doing, please contact Courtney for more information.

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Example images. From Hodges et al., Science, 2009. Biophysical characterization of chromatin regulatory systems will require experiments on intact, living cells.